AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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swallowwly
September 08, 2020 12:24PM
Hi AFNI team,

I had trouble aligning anatomy with vr_base. The following is my code:

align_epi_anat.py -anat2epi -anat FreqAP05_MPRAGE_c1234_U+orig \
-save_skullstrip -suffix _al_junk \
-epi vr_base+orig -epi_base 0 \
-epi_strip 3dAutomask \
-ginormous_move \
-volreg off -tshift off

The alignment result (*al_junk) is usually that the brain is rotated off by some angles and mismatch the anatomy brain (see attached).

I'm using Unifized data. I've tried different ways including: skull-stripping before aligning, different cost functions (lpa, lpc/+zz and others), other skull-strip method, various movement level (big_move, ginormous_move etc.) and none of these could align well (some was able to improve it to some extent).

I never had this problem before with other subjects, so not sure why this one would happen.

Can you please help with this? Thanks!

-Lingyan
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Alignment problem Attachments

swallowwly September 08, 2020 12:24PM

Re: Alignment problem

rick reynolds September 08, 2020 01:45PM